Contacts of the strand formed by residues 160 - 166 (chain C) in PDB entry 3LUE


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 160 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  PRO*     3.2     7.3    -      -       -      +
    110C  LEU*     3.4     0.3    -      -       -      +
    153C  MET*     3.5    19.5    -      -       -      -
    154C  ASP      3.1    11.9    -      -       -      +
    155C  SER*     2.9    19.1    +      -       -      +
    159C  VAL*     1.3    74.2    -      -       -      +
    161C  HIS*     1.3    63.5    +      -       -      +
    162C  THR*     5.3     0.9    -      -       +      -
    177C  ARG*     3.3     4.0    -      -       -      -
    178C  LEU*     2.7    43.5    +      -       +      -
    180C  LEU      2.8    22.0    +      -       -      -
    261C  LEU*     5.0     0.5    -      -       -      +
    274C  ILE*     3.4    28.3    -      -       +      +
    277C  THR*     6.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 161 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  PRO*     1.6    40.4    -      -       +      +
    110C  LEU*     2.1    39.9    +      -       -      -
    136C  ILE*     4.2    20.7    -      -       +      +
    138C  ALA*     4.7     0.7    -      -       -      +
    152C  VAL      3.7     1.2    -      -       -      +
    153C  MET*     3.5     2.9    -      -       -      -
    154C  ASP*     2.9    33.8    +      -       +      +
    160C  THR*     1.3    75.5    -      -       -      +
    162C  THR*     1.3    65.1    +      -       -      +
    163C  VAL*     3.9    15.7    -      -       +      +
    175C  ILE*     3.3    23.8    -      -       +      +
    176C  LEU      3.0    17.5    -      -       -      +
    177C  ARG*     3.3    13.7    -      -       +      +
    277C  THR*     6.0     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 162 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151C  ILE*     4.3     4.7    -      -       +      -
    152C  VAL      3.4     5.4    -      -       -      +
    153C  MET*     3.6    19.7    -      -       +      -
    160C  THR*     5.3     1.6    -      -       +      -
    161C  HIS*     1.3    77.5    -      -       -      +
    163C  VAL*     1.3    60.7    +      -       -      +
    175C  ILE*     3.3     6.2    -      -       -      +
    176C  LEU*     3.0    29.1    +      -       -      +
    274C  ILE*     4.9     1.1    -      -       +      +
    277C  THR*     3.4    25.2    +      -       +      +
    278C  THR*     3.4    38.6    -      -       +      +
    281C  SER*     3.0    25.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 163 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  ILE*     5.4     2.0    -      -       +      -
    138C  ALA*     5.0     6.7    -      -       +      -
    139C  VAL*     3.6    33.9    -      -       +      -
    151C  ILE*     3.2    24.0    -      -       -      +
    152C  VAL*     3.2    16.3    +      -       +      +
    161C  HIS*     3.9    20.9    -      -       +      +
    162C  THR*     1.3    78.0    -      -       -      +
    164C  PRO*     1.3    60.7    -      -       -      +
    165C  ILE*     3.8    16.3    +      -       +      +
    170C  ALA*     3.8    22.9    -      -       +      -
    175C  ILE*     4.0    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 164 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150C  GLY      3.8     5.4    -      -       -      +
    151C  ILE*     4.0     7.2    -      -       +      -
    162C  THR      4.1     0.2    -      -       -      +
    163C  VAL*     1.3    83.6    -      -       -      +
    165C  ILE*     1.3    55.6    +      -       -      +
    170C  ALA*     3.5     2.3    -      -       -      -
    171C  LEU*     2.7    42.5    +      -       +      +
    174C  ALA*     3.5    31.0    -      -       +      +
    175C  ILE*     4.1     2.9    -      -       +      +
    281C  SER*     3.8    13.9    -      -       -      -
    285C  CYS*     3.2    37.2    -      -       -      -
    293C  LEU*     3.8    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 165 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  VAL*     2.1    19.5    -      -       -      +
     44A  MET*     1.3   112.4    -      -       +      +
     61A  LYS*     3.1     5.7    -      -       -      -
    139C  VAL*     5.3     4.3    -      -       +      -
    142C  LEU*     1.5    58.3    -      -       +      -
    148C  THR      3.4     0.9    -      -       -      +
    149C  THR*     3.2     0.3    -      -       -      +
    150C  GLY      2.9    16.6    +      -       -      +
    152C  VAL*     4.1     5.2    -      -       +      -
    163C  VAL*     3.9    20.9    -      -       +      +
    164C  PRO*     1.3    74.6    -      -       -      +
    166C  TYR*     1.3    55.9    +      -       -      +
    169C  TYR      3.2     6.5    -      -       -      +
    170C  ALA*     3.8    13.7    -      -       +      -
    171C  LEU*     4.7     0.7    -      -       -      -
    293C  LEU*     4.1     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 166 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  TYR*     3.0     2.6    -      -       -      -
     57A  GLU      2.1    27.8    -      -       -      -
     58A  ALA*     1.5    50.0    -      -       -      +
     61A  LYS*     0.8   349.1    -      -       +      +
     64A  ILE*     3.0    19.3    -      -       +      +
     65A  LEU*     2.3    44.4    -      -       +      +
    165C  ILE*     1.3    61.5    -      -       -      +
    167C  GLU*     1.3    71.2    +      -       +      +
    168C  GLY      3.4     0.2    -      -       -      -
    169C  TYR*     2.9    27.6    +      -       -      +
    289C  ILE*     3.8     2.2    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il